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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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Report generated on 2024-11-21, 23:29 UTC based on data in: /home/mf019/longread_pangenome/expanded_dataset_analysis

General Statistics

Showing ⁰/₁₅₇ rows and ⁸/₈ columns.

Sample Name	N50 (Kbp)	Assembly Length (Mbp)	# contigs	# bases	# CDS	% Borreliella burgdorferi	% Top 5 Species	% Unclassified
B331PP	903.7Kbp	1.4Mbp	19	1409078	1379
B331PP-checkpoint			19	1409078	1379
B418PP	902.8Kbp	1.4Mbp	18	1376853	1336
B500PP	903.7Kbp	1.4Mbp	19	1429303	1402
ESI26H	910.4Kbp	1.3Mbp	64	1276481	1213
ESI36H	909.9Kbp	1.2Mbp	11	1182078	1118
ESI403H	910.4Kbp	1.4Mbp	34	1364813	1338
ESI425H	342.8Kbp	1.3Mbp	21	1260215	1199
GCA_002151465.1_ASM215146v1_genomic	909.9Kbp	1.3Mbp	12	1288112	1274
GCA_002151485.1_ASM215148v1_genomic	910.7Kbp	1.3Mbp	11	1301554	1305
GCA_002151505.1_ASM215150v1_genomic	909.9Kbp	1.3Mbp	13	1341182	1339
GCA_002442595.2_ASM244259v2_genomic	903.7Kbp	1.4Mbp	19	1409089	1379
GCA_003367295.1_ASM336729v1_genomic	908.5Kbp	1.3Mbp	16	1280240	1237
GCA_019134655.1_ASM1913465v1_genomic	910.0Kbp	1.2Mbp	11	1217256	1168
GCA_019464575.1_ASM1946457v1_genomic	903.7Kbp	1.4Mbp	19	1429304	1405
GCA_024662155.1_ASM2466215v1_genomic	903.2Kbp	1.4Mbp	18	1392060	1357
GCA_024662175.1_ASM2466217v1_genomic	920.8Kbp	1.4Mbp	18	1417706	1400
GCA_024662195.1_ASM2466219v1_genomic	909.7Kbp	1.5Mbp	21	1513701	1505
GCA_030439605.1_ASM3043960v1_genomic	910.7Kbp	1.0Mbp	4	1007753	919
GCA_030439625.1_ASM3043962v1_genomic	910.4Kbp	1.0Mbp	4	1007827	918
GCA_030439665.1_ASM3043966v1_genomic	902.8Kbp	1.0Mbp	4	1000122	915
GCA_030440345.1_ASM3044034v1_genomic	907.8Kbp	1.0Mbp	4	1006065	918
GCA_030444985.1_ASM3044498v1_genomic	910.6Kbp	1.0Mbp	4	1007632	917
GCA_030445005.1_ASM3044500v1_genomic	910.4Kbp	1.0Mbp	4	1007828	918
GCA_030445025.1_ASM3044502v1_genomic	910.7Kbp	1.0Mbp	4	1008124	919
GCA_030445065.1_ASM3044506v1_genomic	910.2Kbp	1.0Mbp	4	1006503	920
GCA_032595375.1_ASM3259537v1_genomic	909.6Kbp	1.0Mbp	4	1007086	922
GCA_032595515.1_ASM3259551v1_genomic	911.4Kbp	1.0Mbp	4	1004596	903
GCA_032595535.1_ASM3259553v1_genomic	909.7Kbp	1.0Mbp	4	1005759	907
GCA_032595755.1_ASM3259575v1_genomic	910.1Kbp	1.0Mbp	4	1006563	882
GCA_038801875.1_ASM3880187v1_genomic	920.0Kbp	0.9Mbp	2	946504	846
GCA_040790715.1_ASM4079071v1_genomic	908.7Kbp	1.3Mbp	14	1289159	1216
GCA_040790735.1_ASM4079073v1_genomic	909.5Kbp	1.4Mbp	18	1391486	1359
GCA_040790745.1_ASM4079074v1_genomic	902.8Kbp	1.4Mbp	18	1371468	1331
GCA_040790755.1_ASM4079075v1_genomic	902.7Kbp	1.3Mbp	16	1321156	1300
GCA_040790765.1_ASM4079076v1_genomic	910.1Kbp	1.4Mbp	19	1397896	1369
GCA_040790775.1_ASM4079077v1_genomic	907.6Kbp	1.4Mbp	17	1417953	1383
GCA_040790785.1_ASM4079078v1_genomic	910.0Kbp	1.4Mbp	18	1383845	1347
GCA_040790795.1_ASM4079079v1_genomic	916.8Kbp	1.3Mbp	16	1325608	1251
GCA_040790805.1_ASM4079080v1_genomic	907.9Kbp	1.2Mbp	12	1216633	1169
GCA_040819585.1_PFhe_I_PB_Ill_cons_genomic	910.3Kbp	1.3Mbp	15	1341511	1317
GCF_000008685.2_ASM868v2_genomic	910.7Kbp	1.5Mbp	22	1521208	1508
GCF_000021405.1_ASM2140v1_genomic	906.7Kbp	1.3Mbp	15	1345494	1327
GCF_000166635.1_ASM16663v1_genomic	902.2Kbp	1.3Mbp	17	1339539	1311
GCF_000166655.1_ASM16665v1_genomic	922.8Kbp	1.5Mbp	21	1531091	1519
GCF_000171735.2_ASM17173v2_genomic	85.3Kbp	1.5Mbp	27	1453013	1441
GCF_000172295.2_ASM17229v2_genomic	35.7Kbp	1.3Mbp	53	1344204	1302
GCF_000172315.2_ASM17231v2_genomic	83.1Kbp	1.3Mbp	26	1294354	1252
GCF_000172335.2_ASM17233v2_genomic	169.2Kbp	1.5Mbp	24	1485884	1475
GCF_000181555.2_ASM18155v2_genomic	908.8Kbp	1.5Mbp	32	1469834	1418
GCF_000181575.2_ASM18157v2_genomic	171.0Kbp	1.3Mbp	20	1321434	1306
GCF_000181715.2_ASM18171v2_genomic	169.5Kbp	1.3Mbp	25	1295451	1255
GCF_000181855.2_ASM18185v2_genomic	37.0Kbp	1.4Mbp	54	1427907	1411
GCF_002151465.1_ASM215146v1_genomic	909.9Kbp	1.3Mbp	12	1288112	1274
GCF_002151485.1_ASM215148v1_genomic	910.7Kbp	1.3Mbp	11	1301554	1305
GCF_002151505.1_ASM215150v1_genomic	909.9Kbp	1.3Mbp	13	1341182	1339
GCF_002442595.2_ASM244259v2_genomic	903.7Kbp	1.4Mbp	19	1409089	1379
GCF_003367295.1_ASM336729v1_genomic	908.5Kbp	1.3Mbp	16	1280240	1237
GCF_019134655.1_ASM1913465v1_genomic	910.0Kbp	1.2Mbp	11	1217256	1168
GCF_019464575.1_ASM1946457v1_genomic	903.7Kbp	1.4Mbp	19	1429304	1405
GCF_024662155.1_ASM2466215v1_genomic	903.2Kbp	1.4Mbp	18	1392060	1357
GCF_024662175.1_ASM2466217v1_genomic	920.8Kbp	1.4Mbp	18	1417706	1400
GCF_024662195.1_ASM2466219v1_genomic	909.7Kbp	1.5Mbp	21	1513701	1505
GCF_040790715.1_ASM4079071v1_genomic	908.7Kbp	1.3Mbp	14	1289159	1216
GCF_040790735.1_ASM4079073v1_genomic	909.5Kbp	1.4Mbp	18	1391486	1359
GCF_040790745.1_ASM4079074v1_genomic	902.8Kbp	1.4Mbp	18	1371468	1331
GCF_040790755.1_ASM4079075v1_genomic	902.7Kbp	1.3Mbp	16	1321156	1300
GCF_040790765.1_ASM4079076v1_genomic	910.1Kbp	1.4Mbp	19	1397896	1369
GCF_040790775.1_ASM4079077v1_genomic	907.6Kbp	1.4Mbp	17	1417953	1383
GCF_040790785.1_ASM4079078v1_genomic	910.0Kbp	1.4Mbp	18	1383845	1347
GCF_040790795.1_ASM4079079v1_genomic	916.8Kbp	1.3Mbp	16	1325608	1251
GCF_040790805.1_ASM4079080v1_genomic	907.9Kbp	1.2Mbp	12	1216633	1169
GCF_040819585.1_PFhe_I_PB_Ill_cons_genomic	910.3Kbp	1.3Mbp	15	1341511	1317
K89HH	274.3Kbp	1.5Mbp	150	1557782	1479
UCT109H	910.6Kbp	1.5Mbp	28	1476377	1438
UCT110H	906.8Kbp	1.4Mbp	114	1417187	1343
UCT113H	905.8Kbp	1.3Mbp	253	1304891	1189	82.6%	83.8%	1.2%
UCT113H_kraken2						82.6%	83.8%	1.2%
UCT124H	900.9Kbp	1.5Mbp	50	1510565	1476
UCT29H	910.5Kbp	1.6Mbp	24	1559716	1547
UCT30H	905.5Kbp	1.5Mbp	89	1471861	1385	83.1%	85.4%	1.1%
UCT30H_kraken2						83.1%	85.4%	1.1%
UCT31H	910.6Kbp	1.5Mbp	32	1531745	1514
UCT32H	921.1Kbp	1.5Mbp	57	1501989	1459	86.0%	86.0%	1.8%
UCT32H_kraken2						86.0%	86.0%	1.8%
UCT35H	910.0Kbp	1.3Mbp	33	1350407	1278	78.8%	87.9%	9.1%
UCT35H_kraken2						78.8%	87.9%	9.1%
UCT50H	902.8Kbp	1.3Mbp	90	1341231	1284	72.2%	77.8%	4.4%
UCT50H_kraken2						72.2%	77.8%	4.4%
UCT92H	906.7Kbp	1.5Mbp	62	1537760	1512	95.2%	96.8%	1.6%
UCT92H_kraken2						95.2%	96.8%	1.6%
UCT95H	893.6Kbp	1.5Mbp	15	1491903	3042
UCT96H	900.9Kbp	1.5Mbp	35	1481271	1451
UNY1032P	910.6Kbp	1.5Mbp	18	1459435	1428
UNY1038P	915.7Kbp	1.4Mbp	19	1403595	1354
UNY1083P	923.1Kbp	1.4Mbp	226	1494188	1405	56.2%	56.6%	30.5%
UNY1083P_kraken2						56.2%	56.6%	30.5%
UNY1085P	903.4Kbp	1.4Mbp	18	1409080	1350
UNY1090P	912.7Kbp	1.4Mbp	19	1413250	1377
UNY1128P	213.8Kbp	1.4Mbp	277	1488312	1399	75.8%	76.2%	5.1%
UNY1128P_kraken2						75.8%	76.2%	5.1%
UNY149P	915.7Kbp	1.4Mbp	19	1427032	1389
UNY169P	902.8Kbp	1.3Mbp	17	1346761	1303
UNY172P	903.4Kbp	1.4Mbp	16	1352494	1298
UNY193P	910.1Kbp	1.4Mbp	19	1403883	1358
UNY203P	910.1Kbp	1.3Mbp	17	1326072	1289
UNY208P	912.7Kbp	1.4Mbp	19	1413253	1376
UNY990P	902.8Kbp	1.4Mbp	17	1367194	1301
URI101H	910.5Kbp	1.6Mbp	32	1554475	1513
URI102H	910.6Kbp	1.4Mbp	44	1442774	1392
URI103H	921.1Kbp	1.5Mbp	56	1474413	1424
URI107H	910.6Kbp	1.5Mbp	49	1505434	1479
URI111H	910.6Kbp	1.5Mbp	23	1539609	1513
URI112H	903.1Kbp	1.4Mbp	85	1431440	1366	82.4%	85.9%	2.4%
URI112H_kraken2						82.4%	85.9%	2.4%
URI117H	434.9Kbp	1.4Mbp	160	1384478	1299	84.4%	85.6%	1.2%
URI117H_kraken2						84.4%	85.6%	1.2%
URI118H	921.0Kbp	1.4Mbp	109	1380118	1317
URI120H	910.7Kbp	1.6Mbp	105	1576195	1544
URI33H	902.8Kbp	1.3Mbp	44	1353948	1272	90.9%	93.2%	2.3%
URI33H_kraken2						90.9%	93.2%	2.3%
URI34H	910.1Kbp	1.4Mbp	79	1376021	1295	84.8%	86.1%	1.3%
URI34H_kraken2						84.8%	86.1%	1.3%
URI36H	927.7Kbp	1.5Mbp	53	1482383	1423	73.6%	90.6%	7.5%
URI36H_kraken2						73.6%	90.6%	7.5%
URI39H	920.7Kbp	1.6Mbp	28	1557202	1542
URI40H	910.6Kbp	1.5Mbp	82	1509727	1470	72.0%	76.8%	1.2%
URI40H_kraken2						72.0%	76.8%	1.2%
URI41H	914.4Kbp	1.5Mbp	84	1468867	1437
URI42H	910.6Kbp	1.5Mbp	74	1460998	1422
URI44H	921.1Kbp	1.4Mbp	75	1417636	1341	76.0%	81.3%	1.3%
URI44H_kraken2						76.0%	81.3%	1.3%
URI45H	42.8Kbp	1.5Mbp	350	1585394	1458	81.1%	84.0%	0.9%
URI45H_kraken2						81.1%	84.0%	0.9%
URI46H	906.8Kbp	1.4Mbp	95	1437550	1363	87.4%	90.5%	1.1%
URI46H_kraken2						87.4%	90.5%	1.1%
URI47H	921.2Kbp	1.5Mbp	29	1512039	1477
URI48H	902.8Kbp	1.4Mbp	22	1377993	1323	95.5%	95.5%	4.5%
URI48H_kraken2						95.5%	95.5%	4.5%
URI56H	903.3Kbp	1.3Mbp	230	1297641	1187
URI86H	919.1Kbp	1.4Mbp	88	1406230	1329
URI87H	910.6Kbp	1.5Mbp	66	1505755	1466
URI88H	906.7Kbp	1.5Mbp	33	1540602	1502
URI89H	910.7Kbp	1.5Mbp	85	1553229	1526	74.1%	77.6%	1.2%
URI89H_kraken2						74.1%	77.6%	1.2%
URI91H	910.7Kbp	1.6Mbp	26	1588266	1574
URI93H	910.6Kbp	1.5Mbp	29	1474340	1426
UWI247P	912.3Kbp	1.4Mbp	17	1359286	1300
UWI248P	910.0Kbp	1.4Mbp	18	1387586	1337
UWI263P	907.9Kbp	1.4Mbp	19	1409038	1372
UWI283P	903.4Kbp	1.3Mbp	16	1332290	1277
XYZ459H	903.2Kbp	1.3Mbp	24	1272095	1199	79.2%	91.7%	8.3%
XYZ459H_kraken2						79.2%	91.7%	8.3%
roary_pangenome_v5_filtered_nsp			2115	1671363	1833
roary_pangenome_v5_filtered_sp			4673	3347826	4137
roary_pangenome_v5_nsp			2762	1769304	1911
roary_pangenome_v5_nsp-checkpoint			2762	1769304	1911

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly (kilo base pairs)	`quast-N50`
\|\|	QUAST	Assembly Length (Mbp)	The total number of bases in the assembly (Mbp).	`quast-Total_length`
\|\|	Bakta	# contigs	Number of contigs	`bakta-Count`
\|\|	Bakta	# bases	Total number of bases in the contigs	`bakta-Length`
\|\|	Bakta	# CDS	Number of found CDS	`bakta-CDSs`	gene_count
\|\|	Kraken	% Borreliella burgdorferi	Percentage of reads that were the top Species over all samples - Borreliella burgdorferi	`kraken-pct_top_one`
\|\|	Kraken	% Top 5 Species	Percentage of reads that were classified by one of the top-5 Species (Borreliella burgdorferi, Borreliella bissettiae, Borreliella mayonii, Borreliella valaisiana, Borreliella garinii)	`kraken-pct_top_n`
\|\|	Kraken	% Unclassified	Percentage of reads that were unclassified	`kraken-pct_unclassified`

QUAST

Quality assessment tool for genome assemblies.URL: http://quast.bioinf.spbau.ruDOI: 10.1093/bioinformatics/btt086

Assembly Statistics

Showing ⁰/₁₃₂ rows and ⁸/₈ columns.

Sample Name	N50 (Kbp)	L50 (K)	Largest contig (Kbp)	Length (Mbp)	Misassemblies	Mismatches/100kbp	Indels/100kbp	Genome Fraction
B331PP	903.7Kbp	0.0K	903.7Kbp	1.4Mbp	24	932.37	60.88	78.8%
B418PP	902.8Kbp	0.0K	902.8Kbp	1.4Mbp	16	851.29	51.15	80.2%
B500PP	903.7Kbp	0.0K	903.7Kbp	1.4Mbp	36	988.31	69.57	82.5%
ESI26H	910.4Kbp	0.0K	910.4Kbp	1.3Mbp	14	488.39	31.81	72.9%
ESI36H	909.9Kbp	0.0K	909.9Kbp	1.2Mbp	14	738.26	33.18	72.1%
ESI403H	910.4Kbp	0.0K	910.4Kbp	1.4Mbp	10	541.99	35.63	83.1%
ESI425H	342.8Kbp	0.0K	434.8Kbp	1.3Mbp	12	813.35	39.89	73.8%
GCA_002151465.1_ASM215146v1_genomic	909.9Kbp	0.0K	909.9Kbp	1.3Mbp	1	44.27	10.74	82.7%
GCA_002151485.1_ASM215148v1_genomic	910.7Kbp	0.0K	910.7Kbp	1.3Mbp	4	110.48	14.05	83.1%
GCA_002151505.1_ASM215150v1_genomic	909.9Kbp	0.0K	909.9Kbp	1.3Mbp	2	93.47	15.29	85.5%
GCA_002442595.2_ASM244259v2_genomic	903.7Kbp	0.0K	903.7Kbp	1.4Mbp	24	932.37	60.88	78.8%
GCA_003367295.1_ASM336729v1_genomic	908.5Kbp	0.0K	908.5Kbp	1.3Mbp	16	758.69	44.05	75.0%
GCA_019134655.1_ASM1913465v1_genomic	910.0Kbp	0.0K	910.0Kbp	1.2Mbp	13	837.36	39.56	73.3%
GCA_019464575.1_ASM1946457v1_genomic	903.7Kbp	0.0K	903.7Kbp	1.4Mbp	30	948.06	69.76	81.1%
GCA_024662155.1_ASM2466215v1_genomic	903.2Kbp	0.0K	903.2Kbp	1.4Mbp	23	892.56	59.71	79.5%
GCA_024662175.1_ASM2466217v1_genomic	920.8Kbp	0.0K	920.8Kbp	1.4Mbp	18	844.86	51.95	78.7%
GCA_024662195.1_ASM2466219v1_genomic	909.7Kbp	0.0K	909.7Kbp	1.5Mbp	0	1.98	4.36	99.4%
GCA_030439605.1_ASM3043960v1_genomic	910.7Kbp	0.0K	910.7Kbp	1.0Mbp	0	3.28	3.37	66.2%
GCA_030439625.1_ASM3043962v1_genomic	910.4Kbp	0.0K	910.4Kbp	1.0Mbp	1	331.98	17.27	66.2%
GCA_030439665.1_ASM3043966v1_genomic	902.8Kbp	0.0K	902.8Kbp	1.0Mbp	1	551.26	21.27	65.6%
GCA_030440345.1_ASM3044034v1_genomic	907.8Kbp	0.0K	907.8Kbp	1.0Mbp	1	529.06	19.61	65.4%
GCA_030444985.1_ASM3044498v1_genomic	910.6Kbp	0.0K	910.6Kbp	1.0Mbp	0	8.73	4.07	66.2%
GCA_030445005.1_ASM3044500v1_genomic	910.4Kbp	0.0K	910.4Kbp	1.0Mbp	1	331.98	17.17	66.2%
GCA_030445025.1_ASM3044502v1_genomic	910.7Kbp	0.0K	910.7Kbp	1.0Mbp	1	337.59	16.97	66.2%
GCA_030445065.1_ASM3044506v1_genomic	910.2Kbp	0.0K	910.2Kbp	1.0Mbp	1	286.20	12.82	66.1%
GCA_032595375.1_ASM3259537v1_genomic	909.6Kbp	0.0K	909.6Kbp	1.0Mbp	1	347.73	17.68	66.2%
GCA_032595515.1_ASM3259551v1_genomic	911.4Kbp	0.0K	911.4Kbp	1.0Mbp	2	338.46	17.20	65.2%
GCA_032595535.1_ASM3259553v1_genomic	909.7Kbp	0.0K	909.7Kbp	1.0Mbp	2	569.01	19.27	64.8%
GCA_032595755.1_ASM3259575v1_genomic	910.1Kbp	0.0K	910.1Kbp	1.0Mbp	0	586.83	24.44	62.7%
GCA_038801875.1_ASM3880187v1_genomic	920.0Kbp	0.0K	920.0Kbp	0.9Mbp	1	522.63	18.34	62.0%
GCA_040790715.1_ASM4079071v1_genomic	908.7Kbp	0.0K	908.7Kbp	1.3Mbp	20	730.03	47.72	77.2%
GCA_040790735.1_ASM4079073v1_genomic	909.5Kbp	0.0K	909.5Kbp	1.4Mbp	20	833.46	45.12	78.7%
GCA_040790745.1_ASM4079074v1_genomic	902.8Kbp	0.0K	902.8Kbp	1.4Mbp	18	860.85	53.89	81.0%
GCA_040790755.1_ASM4079075v1_genomic	902.7Kbp	0.0K	902.7Kbp	1.3Mbp	21	838.73	53.63	80.8%
GCA_040790765.1_ASM4079076v1_genomic	910.1Kbp	0.0K	910.1Kbp	1.4Mbp	16	832.72	44.26	77.7%
GCA_040790775.1_ASM4079077v1_genomic	907.6Kbp	0.0K	907.6Kbp	1.4Mbp	4	1.06	3.96	92.9%
GCA_040790785.1_ASM4079078v1_genomic	910.0Kbp	0.0K	910.0Kbp	1.4Mbp	14	813.36	47.49	78.8%
GCA_040790795.1_ASM4079079v1_genomic	916.8Kbp	0.0K	916.8Kbp	1.3Mbp	15	684.36	44.78	76.1%
GCA_040790805.1_ASM4079080v1_genomic	907.9Kbp	0.0K	907.9Kbp	1.2Mbp	4	51.83	13.27	79.7%
GCA_040819585.1_PFhe_I_PB_Ill_cons_genomic	910.3Kbp	0.0K	910.3Kbp	1.3Mbp	4	525.65	34.93	78.5%
GCF_000008685.2_ASM868v2_genomic	910.7Kbp	0.0K	910.7Kbp	1.5Mbp	0	0.00	0.00	100.0%
GCF_000021405.1_ASM2140v1_genomic	906.7Kbp	0.0K	906.7Kbp	1.3Mbp	7	511.34	38.10	83.3%
GCF_000166635.1_ASM16663v1_genomic	902.2Kbp	0.0K	902.2Kbp	1.3Mbp	15	825.88	48.73	79.1%
GCF_000166655.1_ASM16665v1_genomic	922.8Kbp	0.0K	922.8Kbp	1.5Mbp	29	992.45	62.44	80.6%
GCF_000171735.2_ASM17173v2_genomic	85.3Kbp	0.0K	231.4Kbp	1.5Mbp	16	811.09	42.01	78.2%
GCF_000172295.2_ASM17229v2_genomic	35.7Kbp	0.0K	88.9Kbp	1.3Mbp	9	850.71	63.80	77.5%
GCF_000172315.2_ASM17231v2_genomic	83.1Kbp	0.0K	209.2Kbp	1.3Mbp	9	697.00	38.81	74.4%
GCF_000172335.2_ASM17233v2_genomic	169.2Kbp	0.0K	408.6Kbp	1.5Mbp	12	444.76	34.50	88.2%
GCF_000181555.2_ASM18155v2_genomic	908.8Kbp	0.0K	908.8Kbp	1.5Mbp	18	881.52	57.29	79.3%
GCF_000181575.2_ASM18157v2_genomic	171.0Kbp	0.0K	471.2Kbp	1.3Mbp	10	571.41	34.76	77.4%
GCF_000181715.2_ASM18171v2_genomic	169.5Kbp	0.0K	216.3Kbp	1.3Mbp	16	778.57	42.03	76.3%
GCF_000181855.2_ASM18185v2_genomic	37.0Kbp	0.0K	147.8Kbp	1.4Mbp	24	939.06	76.21	80.4%
GCF_002151465.1_ASM215146v1_genomic	909.9Kbp	0.0K	909.9Kbp	1.3Mbp	1	44.27	10.74	82.7%
GCF_002151485.1_ASM215148v1_genomic	910.7Kbp	0.0K	910.7Kbp	1.3Mbp	4	110.48	14.05	83.1%
GCF_002151505.1_ASM215150v1_genomic	909.9Kbp	0.0K	909.9Kbp	1.3Mbp	2	93.47	15.29	85.5%
GCF_002442595.2_ASM244259v2_genomic	903.7Kbp	0.0K	903.7Kbp	1.4Mbp	24	932.37	60.88	78.8%
GCF_003367295.1_ASM336729v1_genomic	908.5Kbp	0.0K	908.5Kbp	1.3Mbp	16	758.69	44.05	75.0%
GCF_019134655.1_ASM1913465v1_genomic	910.0Kbp	0.0K	910.0Kbp	1.2Mbp	13	837.36	39.56	73.3%
GCF_019464575.1_ASM1946457v1_genomic	903.7Kbp	0.0K	903.7Kbp	1.4Mbp	30	948.06	69.76	81.1%
GCF_024662155.1_ASM2466215v1_genomic	903.2Kbp	0.0K	903.2Kbp	1.4Mbp	23	892.56	59.71	79.5%
GCF_024662175.1_ASM2466217v1_genomic	920.8Kbp	0.0K	920.8Kbp	1.4Mbp	18	844.86	51.95	78.7%
GCF_024662195.1_ASM2466219v1_genomic	909.7Kbp	0.0K	909.7Kbp	1.5Mbp	0	1.98	4.36	99.4%
GCF_040790715.1_ASM4079071v1_genomic	908.7Kbp	0.0K	908.7Kbp	1.3Mbp	20	730.03	47.72	77.2%
GCF_040790735.1_ASM4079073v1_genomic	909.5Kbp	0.0K	909.5Kbp	1.4Mbp	20	833.46	45.12	78.7%
GCF_040790745.1_ASM4079074v1_genomic	902.8Kbp	0.0K	902.8Kbp	1.4Mbp	18	860.85	53.89	81.0%
GCF_040790755.1_ASM4079075v1_genomic	902.7Kbp	0.0K	902.7Kbp	1.3Mbp	21	838.73	53.63	80.8%
GCF_040790765.1_ASM4079076v1_genomic	910.1Kbp	0.0K	910.1Kbp	1.4Mbp	16	832.72	44.26	77.7%
GCF_040790775.1_ASM4079077v1_genomic	907.6Kbp	0.0K	907.6Kbp	1.4Mbp	4	1.06	3.96	92.9%
GCF_040790785.1_ASM4079078v1_genomic	910.0Kbp	0.0K	910.0Kbp	1.4Mbp	14	813.36	47.49	78.8%
GCF_040790795.1_ASM4079079v1_genomic	916.8Kbp	0.0K	916.8Kbp	1.3Mbp	15	684.36	44.78	76.1%
GCF_040790805.1_ASM4079080v1_genomic	907.9Kbp	0.0K	907.9Kbp	1.2Mbp	4	51.83	13.27	79.7%
GCF_040819585.1_PFhe_I_PB_Ill_cons_genomic	910.3Kbp	0.0K	910.3Kbp	1.3Mbp	4	525.65	34.93	78.5%
K89HH	274.3Kbp	0.0K	552.7Kbp	1.5Mbp	20	794.74	55.63	85.1%
UCT109H	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	12	119.40	16.16	93.1%
UCT110H	906.8Kbp	0.0K	906.8Kbp	1.4Mbp	18	747.51	42.21	78.0%
UCT113H	905.8Kbp	0.0K	905.8Kbp	1.3Mbp	19	683.13	35.66	75.1%
UCT124H	900.9Kbp	0.0K	900.9Kbp	1.5Mbp	9	405.69	34.88	90.0%
UCT29H	910.5Kbp	0.0K	910.5Kbp	1.6Mbp	19	224.26	28.36	97.1%
UCT30H	905.5Kbp	0.0K	905.5Kbp	1.5Mbp	30	777.99	55.55	79.2%
UCT31H	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	16	228.94	28.73	94.2%
UCT32H	921.1Kbp	0.0K	921.1Kbp	1.5Mbp	28	932.44	58.02	80.1%
UCT35H	910.0Kbp	0.0K	910.0Kbp	1.3Mbp	19	684.11	34.37	74.8%
UCT50H	902.8Kbp	0.0K	902.8Kbp	1.3Mbp	16	796.43	55.42	78.5%
UCT92H	906.7Kbp	0.0K	906.7Kbp	1.5Mbp	29	909.46	55.27	80.0%
UCT95H	893.6Kbp	0.0K	893.6Kbp	1.5Mbp	20	917.34	850.00	74.4%
UCT96H	900.9Kbp	0.0K	900.9Kbp	1.5Mbp	20	434.17	32.70	90.8%
UNY1032P	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	3	88.25	15.50	93.7%
UNY1038P	915.7Kbp	0.0K	915.7Kbp	1.4Mbp	18	743.29	45.05	78.4%
UNY1083P	923.1Kbp	0.0K	923.1Kbp	1.4Mbp	28	795.09	55.07	80.3%
UNY1085P	903.4Kbp	0.0K	903.4Kbp	1.4Mbp	19	878.26	57.40	79.8%
UNY1090P	912.7Kbp	0.0K	912.7Kbp	1.4Mbp	17	827.41	42.21	79.0%
UNY1128P	213.8Kbp	0.0K	709.5Kbp	1.4Mbp	27	828.82	65.41	81.7%
UNY149P	915.7Kbp	0.0K	915.7Kbp	1.4Mbp	21	841.47	49.76	80.0%
UNY169P	902.8Kbp	0.0K	902.8Kbp	1.3Mbp	18	855.10	53.06	80.4%
UNY172P	903.4Kbp	0.0K	903.4Kbp	1.4Mbp	17	841.18	53.26	79.0%
UNY193P	910.1Kbp	0.0K	910.1Kbp	1.4Mbp	10	769.19	46.76	77.0%
UNY203P	910.1Kbp	0.0K	910.1Kbp	1.3Mbp	15	731.32	33.69	74.6%
UNY208P	912.7Kbp	0.0K	912.7Kbp	1.4Mbp	14	772.90	41.67	78.5%
UNY990P	902.8Kbp	0.0K	902.8Kbp	1.4Mbp	14	807.88	53.28	78.8%
URI101H	910.5Kbp	0.0K	910.5Kbp	1.6Mbp	18	200.18	22.77	94.4%
URI102H	910.6Kbp	0.0K	910.6Kbp	1.4Mbp	10	92.81	11.59	91.2%
URI103H	921.1Kbp	0.0K	921.1Kbp	1.5Mbp	25	869.46	52.92	80.5%
URI107H	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	12	127.59	12.91	93.0%
URI111H	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	21	251.16	28.36	94.2%
URI112H	903.1Kbp	0.0K	903.1Kbp	1.4Mbp	26	827.54	54.85	79.2%
URI117H	434.9Kbp	0.0K	461.8Kbp	1.4Mbp	16	738.38	49.21	76.7%
URI118H	921.0Kbp	0.0K	921.0Kbp	1.4Mbp	21	777.62	48.77	78.8%
URI120H	910.7Kbp	0.0K	910.7Kbp	1.6Mbp	15	241.92	30.56	94.7%
URI33H	902.8Kbp	0.0K	902.8Kbp	1.3Mbp	18	777.30	49.44	79.8%
URI34H	910.1Kbp	0.0K	910.1Kbp	1.4Mbp	9	704.15	41.21	75.9%
URI36H	927.7Kbp	0.0K	927.7Kbp	1.5Mbp	39	973.06	63.98	82.6%
URI39H	920.7Kbp	0.0K	920.7Kbp	1.6Mbp	15	216.20	22.67	96.5%
URI40H	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	15	147.59	20.18	93.4%
URI41H	914.4Kbp	0.0K	914.4Kbp	1.5Mbp	13	166.82	22.52	91.7%
URI42H	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	12	153.47	20.25	90.3%
URI44H	921.1Kbp	0.0K	921.1Kbp	1.4Mbp	24	798.63	51.27	78.8%
URI45H	42.8Kbp	0.0K	254.7Kbp	1.5Mbp	21	859.07	53.87	80.8%
URI46H	906.8Kbp	0.0K	906.8Kbp	1.4Mbp	29	817.66	52.04	79.3%
URI47H	921.2Kbp	0.0K	921.2Kbp	1.5Mbp	31	924.47	58.01	80.9%
URI48H	902.8Kbp	0.0K	902.8Kbp	1.4Mbp	18	854.78	48.47	79.7%
URI56H	903.3Kbp	0.0K	903.3Kbp	1.3Mbp	14	728.86	48.69	77.9%
URI86H	919.1Kbp	0.0K	919.1Kbp	1.4Mbp	24	763.12	43.83	78.0%
URI87H	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	12	152.86	15.37	93.8%
URI88H	906.7Kbp	0.0K	906.7Kbp	1.5Mbp	34	919.68	56.37	81.5%
URI89H	910.7Kbp	0.0K	910.7Kbp	1.5Mbp	17	195.47	23.38	94.1%
URI91H	910.7Kbp	0.0K	910.7Kbp	1.6Mbp	12	114.59	13.08	96.1%
URI93H	910.6Kbp	0.0K	910.6Kbp	1.5Mbp	15	137.80	21.54	93.4%
UWI247P	912.3Kbp	0.0K	912.3Kbp	1.4Mbp	16	747.05	44.21	76.9%
UWI248P	910.0Kbp	0.0K	910.0Kbp	1.4Mbp	18	784.23	52.06	77.0%
UWI263P	907.9Kbp	0.0K	907.9Kbp	1.4Mbp	25	829.11	51.82	78.6%
UWI283P	903.4Kbp	0.0K	903.4Kbp	1.3Mbp	20	872.33	51.52	77.2%
XYZ459H	903.2Kbp	0.0K	903.2Kbp	1.3Mbp	8	757.97	44.71	75.2%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: quast_table_table

Sort	Group	Column	Description	ID
\|\|	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly.	`quast-N50`
\|\|	QUAST	L50 (K)	L50 is the number of contigs larger than N50, i.e. the minimum number of contigs comprising 50% of the total assembly length.	`quast-L50`
\|\|	QUAST	Largest contig (Kbp)	The size of the largest contig of the assembly	`quast-Largest_contig`
\|\|	QUAST	Length (Mbp)	The total number of bases in the assembly.	`quast-Total_length`
\|\|	QUAST	Misassemblies	The number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).	`quast-misassemblies`
\|\|	QUAST	Mismatches/100kbp	The number of mismatches per 100 kbp	`quast-mismatches_per_100_kbp`
\|\|	QUAST	Indels/100kbp	The number of indels per 100 kbp	`quast-indels_per_100_kbp`
\|\|	QUAST	Genome Fraction	The total number of aligned bases in the reference, divided by the genome size.	`quast-Genome_fraction`

Number of Contigs

This plot shows the number of contigs found for each assembly, broken down by length.

Created with MultiQC

Bakta

Version:


                      
                        1.10.0

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.URL: https://github.com/oschwengers/baktaDOI: 10.1099/mgen.0.000685

This barplot shows the distribution of different types of features found in each sample.

Bakta can detect different features:

tRNAs
tmRNAs
rRNAs
ncRNAs
ncRNA regions
CRISPR arrays
CDSs
pseudogenes
hypotheticals
signal peptides
sORFs
gaps
oriCs
oriVs
oriTs

This barplot shows you the distribution of these different types of features found in each sample.

Created with MultiQC

Kraken

Taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.URL: https://ccb.jhu.edu/software/krakenDOI: 10.1186/gb-2014-15-3-r46

Top taxa

The number of reads falling into the top 5 taxa across different ranks.

To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 5 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.

Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Software	Version
Bakta	`1.10.0`

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General Statistics

General Statistics: Columns

QUAST

Assembly Statistics

QUAST: Assembly Statistics: Columns

Number of Contigs

Bakta

Kraken

Top taxa Help

Software Versions

v1.25

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Top taxa